[English] 日本語
Yorodumi
- PDB-6td7: Structure of truncated hemoglobin THB11 from Chlamydomonas reinhardtii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6td7
TitleStructure of truncated hemoglobin THB11 from Chlamydomonas reinhardtii
ComponentsTHB11
KeywordsOXYGEN BINDING / heme binding / truncated hemoglobin / nitrite reduction / pentacoordination
Function / homology
Function and homology information


thioredoxin peroxidase activity / cell redox homeostasis / oxygen binding / cellular response to oxidative stress / heme binding / cytoplasm
Similarity search - Function
Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globin-like superfamily
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Uncharacterized protein
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsHuwald, D. / Gasper, R. / Hemschemeier, A. / Hofmann, E.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationHE 5790/3-1 Germany
German Research FoundationRTG 2341 Germany
CitationJournal: J.Biol.Inorg.Chem. / Year: 2020
Title: Distinctive structural properties of THB11, a pentacoordinate Chlamydomonas reinhardtii truncated hemoglobin with N- and C-terminal extensions.
Authors: Huwald, D. / Duda, S. / Gasper, R. / Olieric, V. / Hofmann, E. / Hemschemeier, A.
History
DepositionNov 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: THB11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5083
Polymers15,8651
Non-polymers6432
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-25 kcal/mol
Surface area7070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.040, 42.620, 90.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein THB11


Mass: 15865.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_16g662750v5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2K3CTN8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: protein 19 mg*ml-1 in 15 mM Tris-HCl pH 8.0 mixed 1:1 with 0.1 M HEPES pH 7.0, 21% PEG 6.000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.739 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.739 Å / Relative weight: 1
ReflectionResolution: 1.75→38.54 Å / Num. all: 594012 / Num. obs: 11933 / % possible obs: 94.26 % / Redundancy: 49.8 % / Biso Wilson estimate: 17.99 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09463 / Rpim(I) all: 0.01261 / Rrim(I) all: 0.09552 / Net I/σ(I): 38.39
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.5662 / Mean I/σ(I) obs: 2.64 / Num. unique all: 4429 / Num. unique obs: 711 / CC1/2: 0.83 / Rpim(I) all: 0.2366 / Rrim(I) all: 0.6174 / % possible all: 58.37

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSVERSION Nov 1, 2016 BUILT=20161205data reduction
XSCALEVERSION Nov 1, 2016 BUILT=20161205data scaling
PHASER2.7.18phasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→38.54 Å / SU ML: 0.1825 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 19.6183
RfactorNum. reflection% reflection
Rfree0.2097 1194 10.01 %
Rwork0.1732 --
obs-11933 94.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.79 Å2
Refinement stepCycle: LAST / Resolution: 1.75→38.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 45 153 1216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00481145
X-RAY DIFFRACTIONf_angle_d0.89281566
X-RAY DIFFRACTIONf_chiral_restr0.0407156
X-RAY DIFFRACTIONf_plane_restr0.0042200
X-RAY DIFFRACTIONf_dihedral_angle_d15.7041682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.820.3022810.2273734X-RAY DIFFRACTION59.36
1.82-1.90.26241240.19721103X-RAY DIFFRACTION90.15
1.9-20.21551350.1881216X-RAY DIFFRACTION98.54
2-2.130.2191380.16061247X-RAY DIFFRACTION99.35
2.13-2.290.20111390.16211247X-RAY DIFFRACTION100
2.29-2.520.24311400.16781270X-RAY DIFFRACTION99.93
2.52-2.890.19991420.18151267X-RAY DIFFRACTION99.93
2.89-3.640.19741420.1661283X-RAY DIFFRACTION100
3.64-45.130.1971530.17061372X-RAY DIFFRACTION99.93

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more